java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.utilities.AlgorithmSubsample

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmSubsample
extends AlgorithmBase
```
Takes in an image and subsamples it to a new set of dimensions. The subsample image is a Gaussian weighted average of neighboring pixels (voxels) of the original image. For 4D images only the first 3 dimensions are subsampled

Author:

Evan McCreedy

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private ModelImage`	`paddedImage`	Padded image.
`private double[]`	`posRatios`	Ratios used to translate points in the result image to points in the source image.
`private boolean`	`processIndep`	DOCUMENT ME!
`private int[]`	`resultExtents`	Extents the resultImage should have.
`private ModelImage`	`resultImage`	Result image.
`private float[]`	`sigmas`	Std deviation of the Gaussian function.
`private ModelImage`	`srcImage`	Image to subsample from.
`private boolean`	`transformVOI`	DOCUMENT ME!
`private TransMatrix`	`transMatrix`	DOCUMENT ME!
`private boolean`	`trilinearFlag`	Whether to perform trilinear filtering when getting intensities of points on the source image.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmSubsample(ModelImage src, ModelImage result, int[] newExtents, int[] padExtents, float[] _sigmas, boolean indep, boolean transformVOI, TransMatrix transMatrix, boolean doPad)`	Setup for a later subsampling of an image.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private double`	`computeGaussian2D(double locX, double locY, double sigmaX, double sigmaY)`	Compute the value of the 2D gaussian at a point.
`private double`	`computeGaussian3D(double locX, double locY, double locZ, double sigmaX, double sigmaY, double sigmaZ)`	Computes the gaussian weights for a particular point.
`private void`	`computeRatios()`	Computes the image scaling ratios.
`void`	`finalize()`	Prepares this class for destruction.
`private float[]`	`getNearestNeighborPos2D(float x, float y)`	Translates a point from the result image to the source image.
`private float[]`	`getNearestNeighborPos3D(float x, float y, float z)`	Translates a point from the result image to the source image.
`ModelImage`	`getResultImage()`	Return the result image (or null if not created yet).
`private float`	`getTriLinearVal3D(float x, float y, float z, int t, int channelIndex, ModelSimpleImage src)`	Version of get that performs tri-linear interpoloation.
`private float`	`getTriLinearVal3D(float x, float y, float z, int channelIndex, ModelSimpleImage src)`	Version of get that performs tri-linear interpoloation.
`private float`	`getValue2D(float x, float y, float z, int channelIndex, ModelSimpleImage src)`	Get the value of a 2D point.
`private float`	`getValue3D(float x, float y, float z, int t, int channelIndex, ModelSimpleImage src)`	Get the value of a 4D point.
`private float`	`getValue3D(float x, float y, float z, int channelIndex, ModelSimpleImage src)`	Get the value of a 3D point.
`private static java.lang.String`	`makeImageName(java.lang.String image_name, java.lang.String ext)`	Helper method for making the result image's name.
`private ModelImage`	`padImage(ModelImage kImage, int[] padExtents)`
`void`	`runAlgorithm()`	Subsample the image.
`private ModelSimpleImage`	`subsample2D(int nImages)`	Subsample a 2D image.
`private ModelSimpleImage`	`subsample3D()`	Perform the subsampling.
`private ModelSimpleImage`	`subsample4D()`	Perform the subsampling.
`private void`	`transform25DVOI(ModelImage image, float[] imgBuffer, TransMatrix xfrm)`	Transforms and resamples a 2D or 25D VOI using nearest neighbor interpolation.
`private void`	`transform3DVOI(ModelImage image, float[] imgBuffer, TransMatrix xfrm)`	Transforms and resamples a 3D VOI using nearest neighbor interpolation.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - posRatios
```
private double[] posRatios
```
    Ratios used to translate points in the result image to points in the source image.
  - processIndep
```
private boolean processIndep
```
    DOCUMENT ME!
  - resultExtents
```
private int[] resultExtents
```
    Extents the resultImage should have.
  - resultImage
```
private ModelImage resultImage
```
    Result image.
  - paddedImage
```
private ModelImage paddedImage
```
    Padded image.
  - sigmas
```
private float[] sigmas
```
    Std deviation of the Gaussian function.
  - srcImage
```
private ModelImage srcImage
```
    Image to subsample from.
  - transformVOI
```
private boolean transformVOI
```
    DOCUMENT ME!
  - transMatrix
```
private TransMatrix transMatrix
```
    DOCUMENT ME!
  - trilinearFlag
```
private boolean trilinearFlag
```
    Whether to perform trilinear filtering when getting intensities of points on the source image.
- Constructor Detail
  - AlgorithmSubsample
```
public AlgorithmSubsample(ModelImage src,
                          ModelImage result,
                          int[] newExtents,
                          int[] padExtents,
                          float[] _sigmas,
                          boolean indep,
                          boolean transformVOI,
                          TransMatrix transMatrix,
                          boolean doPad)
```
    Setup for a later subsampling of an image.
    
    Parameters:
    
    src - image to be subsampled
    
    result - image created by subsampling
    
    newExtents - dimensions of the result image to be sampled into
    
    _sigmas - x, y, and z scales for the gaussian function
    
    indep - process slices independently (cannot change the z dimension)
    
    transformVOI - if true transform the VOIs
    
    transMatrix - transformation matrix
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getResultImage
```
public ModelImage getResultImage()
```
    Return the result image (or null if not created yet).
    
    Returns:
    
    the subsampled image
  - runAlgorithm
```
public void runAlgorithm()
```
    Subsample the image.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - computeGaussian2D
```
private double computeGaussian2D(double locX,
                                 double locY,
                                 double sigmaX,
                                 double sigmaY)
```
    Compute the value of the 2D gaussian at a point.
    
    Parameters:
    
    locX - x location of the value to compute
    
    locY - y location of the value to compute
    
    sigmaX - standard deviation of the guassian in the x dimension
    
    sigmaY - standard deviation of the guassian in the y dimension
    
    Returns:
    
    the value of the 2D gaussian at the given point
  - computeGaussian3D
```
private double computeGaussian3D(double locX,
                                 double locY,
                                 double locZ,
                                 double sigmaX,
                                 double sigmaY,
                                 double sigmaZ)
```
    Computes the gaussian weights for a particular point. Written by Paul Hemler in AlgorithmVesselSegmenation.
    
    Parameters:
    
    locX - distance to go in the x dir from the point
    
    locY - distance to go in the y dir from the point
    
    locZ - distance to go in the z dir from the point
    
    sigmaX - stddev of the gaussian function in the x dir
    
    sigmaY - stddev of the gaussian function in the y dir
    
    sigmaZ - stddev of the gaussian function in the z dir
    
    Returns:
    
    the gaussian weight coeff.
  - computeRatios
```
private void computeRatios()
```
    Computes the image scaling ratios.
  - getNearestNeighborPos2D
```
private float[] getNearestNeighborPos2D(float x,
                                        float y)
```
    Translates a point from the result image to the source image.
    
    Parameters:
    
    x - x coordinate of point to be translated
    
    y - y coordinate of point to be translated
    
    Returns:
    
    the translated point on the source image
  - getNearestNeighborPos3D
```
private float[] getNearestNeighborPos3D(float x,
                                        float y,
                                        float z)
```
    Translates a point from the result image to the source image.
    
    Parameters:
    
    x - x coordinate of point to be translated
    
    y - y coordinate of point to be translated
    
    z - z coordinate of point to be translated
    
    Returns:
    
    the translated point on the source image
  - getTriLinearVal3D
```
private float getTriLinearVal3D(float x,
                                float y,
                                float z,
                                int channelIndex,
                                ModelSimpleImage src)
```
    Version of get that performs tri-linear interpoloation. Note: does NOT perform bounds checking.
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate
    
    channelIndex - color channel
    
    src - image to get intensity value from
    
    Returns:
    
    the tri-linear interpolated value
  - getTriLinearVal3D
```
private float getTriLinearVal3D(float x,
                                float y,
                                float z,
                                int t,
                                int channelIndex,
                                ModelSimpleImage src)
```
    Version of get that performs tri-linear interpoloation. Note: does NOT perform bounds checking.
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate
    
    t - t coordinate
    
    channelIndex - color channel
    
    src - image to get intensity value from
    
    Returns:
    
    the tri-linear interpolated value
  - getValue2D
```
private float getValue2D(float x,
                         float y,
                         float z,
                         int channelIndex,
                         ModelSimpleImage src)
```
    Get the value of a 2D point.
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate (0 if really 2D)
    
    channelIndex - color channel
    
    src - image to sample from
    
    Returns:
    
    the point's value
  - getValue3D
```
private float getValue3D(float x,
                         float y,
                         float z,
                         int channelIndex,
                         ModelSimpleImage src)
```
    Get the value of a 3D point.
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate
    
    channelIndex - color channel
    
    src - image to sample from
    
    Returns:
    
    the point's value
  - getValue3D
```
private float getValue3D(float x,
                         float y,
                         float z,
                         int t,
                         int channelIndex,
                         ModelSimpleImage src)
```
    Get the value of a 4D point.
    
    Parameters:
    
    x - x coordinate
    
    y - y coordinate
    
    z - z coordinate
    
    t - DOCUMENT ME!
    
    channelIndex - color channel
    
    src - image to sample from
    
    Returns:
    
    the point's value
  - subsample2D
```
private ModelSimpleImage subsample2D(int nImages)
```
    Subsample a 2D image.
    
    Parameters:
    
    nImages - the number of 2D images to subsample (1 if really 2D)
    
    Returns:
    
    the subsampled image
  - subsample3D
```
private ModelSimpleImage subsample3D()
```
    Perform the subsampling. Create a result image with the extents given into the constuctor. Then, for each point in the result image, find point which corresponds to it in the source image. Add up weighted intensities of the neighbors of this point in the source image and the intensity of the point itself. Store this value in the point of the result image. Once all points in the result image have been visted, return the result image.
    
    Returns:
    
    resampled image
  - subsample4D
```
private ModelSimpleImage subsample4D()
```
    Perform the subsampling. Create a result image with the extents given into the constuctor. Then, for each point in the result image, find point which corresponds to it in the source image. Add up weighted intensities of the neighbors of this point in the source image and the intensity of the point itself. Store this value in the point of the result image. Once all points in the result image have been visted, return the result image. Does not subsample in fourth time dimension - 3.5D operation
    
    Returns:
    
    resampled image
  - transform25DVOI
```
private void transform25DVOI(ModelImage image,
                             float[] imgBuffer,
                             TransMatrix xfrm)
```
    Transforms and resamples a 2D or 25D VOI using nearest neighbor interpolation.
    
    Export VOIs as a mask image
    
    Transform mask
    
    Extract VOI contours from mask image and put in new image.
    Parameters:
    
    image - Image where VOIs are stored
    
    imgBuffer - Image array
    
    xfrm - Transformation matrix to be applied
  - transform3DVOI
```
private void transform3DVOI(ModelImage image,
                            float[] imgBuffer,
                            TransMatrix xfrm)
```
    Transforms and resamples a 3D VOI using nearest neighbor interpolation.
    
    Export VOIs as a mask image
    
    Transform mask
    
    Extract VOI contours from mask image and put in new image.
    Parameters:
    
    image - Image where VOIs are stored
    
    imgBuffer - Image array
    
    xfrm - Transformation matrix to be applied
  - padImage
```
private ModelImage padImage(ModelImage kImage,
                            int[] padExtents)
```
  - makeImageName
```
private static java.lang.String makeImageName(java.lang.String image_name,
                                              java.lang.String ext)
```
    Helper method for making the result image's name. Strips the current extension from the original name, adds the given extension, and returns the new name.
    
    Parameters:
    
    image_name - the original image's name
    
    ext - Extension to add which gives information about what algorithm was performed on the image.
    
    Returns:
    
    The new image name.

Class AlgorithmSubsample

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

posRatios

processIndep

resultExtents

resultImage

paddedImage

sigmas

srcImage

transformVOI

transMatrix

trilinearFlag

Constructor Detail

AlgorithmSubsample

Method Detail

finalize

getResultImage

runAlgorithm

computeGaussian2D

computeGaussian3D

computeRatios

getNearestNeighborPos2D

getNearestNeighborPos3D

getTriLinearVal3D

getTriLinearVal3D

getValue2D

getValue3D

getValue3D

subsample2D

subsample3D

subsample4D

transform25DVOI

transform3DVOI

padImage

makeImageName